R Notebook

library(DESeq2)
library(tidyverse)
library(limma)
library(vegan)

load("RData_files/initial_fullddsdesigncountsVsdcountsWGCNA.RData")

remove batch effect of genotype

vsd2 <- removeBatchEffect(assay(Vsd), batch = Vsd$Genotype)

formal analysis of variance in distance matrix (PERMANOVA)